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Should I use robots.txt to do this, or rel=nofollow in my affiliate links?
How about if I am using Redirects in .htaccess for all my affiliate links?
Ie: Redirect: /affiliatelink [affiliate...] company link....
That said, I see NO evidence currently that the SE's are hitting pages with mainly aff links on them, and I certainly see all sorts of examples of pages doing well with only aff links, hard coded, and plain as day.
Your call as to whether you want to guard against some possible future move by the SE's.
I hope search engines don't start discriminating against affiliate sites, since that's what I do for a living! Maybe they are mainly concerned about sites with excessive affiliate links plastered all over their pages, so just 1 or 2 per page should be no problem.